Problems Installing Rmpi on openSUSE 11.1 x86_64
Thanks to Hao, Brian and Martin (offlist) for their suggestions.
I tried them all:
- setting LD_LIBRARY_PATH
- using "--configure-args=--with-mpi=/path_to_lam"
- using mpicc
-> all without success when trying to install Rmpi (same error message as
before)
Since I cannot accept using OpenMPI using 100% CPU power in idle mode, I
still need to get LAM working.
Martin suggested modifiying "configure.ac":
tar xzf Rmpi_0.5-7.tar.gz
vim Rmpi/configure.ac
I added
after line 67: MPITYPE="LAM"
after line 128:
elif test -f ${MPI_ROOT}/lib64/libmpi.so; then #Till
echo "Found libmpi in ${MPI_ROOT}/lib64"
MPI_LIBS="-L${MPI_ROOT}/lib64 -lmpi"
MPI_INCLUDE="${MPI_INCLUDE} ${MPI_INCLUDE}/64"
followed by
cd Rmpi && autoconf && cd ..
R CMD INSTALL --clean Rmpi
compiles without errors (see snippet 1 below).
However, when tryinig to load Rmpi in R I get an error:
library("Rmpi")
Error in dyn.load(file, DLLpath = DLLpath, ...) :
kann shared library
'/home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so'
nicht laden:
/usr/lib64/libmpi.so.0: undefined symbol: lam_ssi_cr_did
Fehler in library("Rmpi") : .First.lib fehlgeschlagen f?r 'Rmpi'
Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
.Platform$dynlib.ext, :
shared library
'/home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so'
wurde nicht geladen
Translation:
library("Rmpi")
Error in dyn.load(file, DLLpath = DLLpath, ...) :
could not load shared library
'/home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so':
/usr/lib64/libmpi.so.0: undefined symbol: lam_ssi_cr_did
Error in library("Rmpi") : .First.lib failed for 'Rmpi'
Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
.Platform$dynlib.ext, :
shared library
'/home/francke/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi/libs/Rmpi.so'
not loaded
"Rmpi.so" exists, so I dunno what's wrong. Any help is appreciated,
Melwin
####snippet: installation of RMPI
* Installing to library
'/home/francke/R/x86_64-unknown-linux-gnu-library/2.8'
* Installing *source* package 'Rmpi' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
I am here /usr
Try to find mpi.h ...
Found in /usr/include
Try to find libmpi.so or libmpich.a
Found libmpi in /usr/lib64
Try to find liblam.so ...
checking for main in -llam... no
liblam not found. Probably not LAM-MPI
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -I/usr/include/64 -DMPI2 -DLAM
-fPIC -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
-fasynchronous-unwind-tables -c conversion.c -o conversion.o
gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -I/usr/include/64 -DMPI2 -DLAM
-fPIC -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
-fasynchronous-unwind-tables -c internal.c -o internal.o
gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -I/usr/include/64 -DMPI2 -DLAM
-fPIC -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
-fasynchronous-unwind-tables -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/include -I/usr/include/64 -DMPI2 -DLAM
-fPIC -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
-fasynchronous-unwind-tables -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so conversion.o
internal.o RegQuery.o Rmpi.o -L/usr/lib64 -lmpi -lutil -lpthread -fPIC
-L/usr/lib64/R/lib -lR
** R
** demo
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'Rmpi'
[...]
** building package indices ...
* DONE (Rmpi)
####end snippet
2009/6/26 Hao Yu <hyu at stats.uwo.ca>:
Hi Melwin, Did you try R CMD INSTALL Rmpi_0.5-7.tar.gz --configure-args=--with-mpi=/path_to_lam Your system may have several mpi and Rmpi did not find a right mpi. BTW, when you are installing lam, make sure to turn dynamic lib on. The default one is static one and Rmpi needs libmpi.so to work. Hao Melwin wrote:
Thanks for the reply. 2009/6/24 Rowe, Brian Lee Yung (Portfolio Analytics) <B_Rowe at ml.com>:
Did you confirm that your MPI installation is working? That is the probably the first step.
LAM seems to work ok: ? ?johnson at linuxmodel:~> lamboot -v ? ?LAM 7.1.4/MPI 2 C++/ROMIO - Indiana University ? ?n-1<4165> ssi:boot:base:linear: booting n0 (localhost) ? ?n-1<4165> ssi:boot:base:linear: finished ? ?johnson at linuxmodel:~> lamexec C hostname ? ?linuxmodel
Regarding LD_LIBRARY_PATH, since I don't know what your configuration is, make sure you export it to your environment and also don't overwrite any existing values. ?i.e. This is better: ?$ export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH since it looks like you're on a 64 bit platform.
Tried that. Same results as before: ? ?johnson at linuxmodel:~> ? ? R CMD INSTALL Rmpi_0.5-7.tar.gz ? ?* Installing to library '/home/johnson/R/x86_64-unknown-linux-gnu-library/2.8' ? ?* Installing *source* package 'Rmpi' ... ? ?checking for gcc... gcc ? ?checking for C compiler default output file name... a.out ? ?checking whether the C compiler works... yes ? ?checking whether we are cross compiling... no ? ?checking for suffix of executables... ? ?checking for suffix of object files... o ? ?checking whether we are using the GNU C compiler... yes ? ?checking whether gcc accepts -g... yes ? ?checking for gcc option to accept ISO C89... none needed ? ?I am here /usr ? ?Try to find mpi.h ... ? ?Found in /usr/include ? ?Try to find libmpi.so or libmpich.a ? ?checking for main in -lmpi... no ? ?libmpi not found. exiting... ? ?ERROR: configuration failed for package 'Rmpi' ? ?** Removing '/home/johnson/R/x86_64-unknown-linux-gnu-library/2.8/Rmpi'
I use OpenMPI and it include an mpi-based compiler which I found to work better than gcc directly. You might try that. Just make sure you export your MPI_ROOT.
I would love to use OpenMPI, but I gather the slave spawning from within R is not yet possible - which is what I need in interactive mode (https://stat.ethz.ch/pipermail/r-sig-hpc/2009-February/000104.html). I'd love to hear that this has changed.
It would also probably help to include a bit more output from the compilation process.
The dump above contains the entire output, I hope that helps. thanks again, Melwin
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